The missing heritability problem, highlighted by genomewide association studies of human disease, is the inability of common genetic variation to fully account for the heritability of complex traits. This proposal deals with one possible explanation for missing heritability: transgenerational inheritance of epigenetic variants independently of genome sequence. Work by one of the PIs and others in plant and animal species has shown that inheritance of epigenetic variants is very different from Mendelian inheritance. However the number of epigenetic variants that can be transmitted from parents to offspring, and the persistence of transmission through multiple generations, have never been systematically studied in animals. The overall goal of this project is to quantify transmissibilityof epigenetic variation through multiple generations. Isogenic mouse strains allow this study to be carried out in conditions that minimize genetic and environmental factors. We are interested in epigenetic variants that have functional consequences: for this reason we will use gene expression variants, in a single homogeneous cell type, as the functional readout of epigenetic variation. Gene expression variants are common in isogenic mice. We hypothesize that gene expression variants can be transmitted through multiple generations, and that such transmission is affected by selection or environmental cues (such as diet). To accept or reject this hypothesis, we will use RNA-Seq to identify gene expression variants in a cohort of isogenic mice, and use these mice as founders of 5-generation pedigrees in which the appearance, disappearance, and transmission of variants will be quantified. In one set of pedigrees, specific expression variants will be selected for breeding; another set will be maintained on a high-fat diet. Finally, we will correlate gene expression variants with methylation variants, and resequence selected mice to assess the true degree of their isogenicity. This study will demonstrate how many epigenetic variants are transmitted from parents to offspring, how stable their transmissibility is through multiple generations, and how transmissibility is affected by selection and the environment.